2PPO

Crystal structure of E60A mutant of FKBP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural coupling between FKBP12 and buried water.

Szep, S.Park, S.Boder, E.T.Van Duyne, G.D.Saven, J.G.

(2009) Proteins 74: 603-611

  • DOI: 10.1002/prot.22176
  • Primary Citation of Related Structures:  2PPN, 2PPP

  • PubMed Abstract: 
  • Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 bind ...

    Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506-binding protein 1A
A
107Homo sapiensGene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 28.793α = 90.00
b = 62.563β = 113.70
c = 32.420γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CCP4phasing
SHELXL-97refinement
CCP4model building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance